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Rigorous understanding of the self-assembly of colloidal nanocrystals is crucial to the development of tailored nanostructured materials. Despite extensive studies, a mechanistic understanding of self-assembly under non-equilibrium driven by an external field remains an ongoing challenge. We demonstrate self-assembly by optical tweezers imposing an external attractive field for cubic-phase sodium yttrium fluoride nanocrystals. We show that surface roughness of the nanocrystals is a decisive factor for contact leading to assembly between the nanocrystals, manifested by the roughness-dependent hydrodynamic resistivity. This provides direct evidence that dynamics are equally important to energetics in understanding self-assembly. These results have implications in a wide variety of different fields, such as in understanding the factors that mediate oriented attachment-based crystal growth or in interpreting the structure of binding sites on viruses., Comment: 21 pages, 3 main figures, 8 supplemental figures, 2 supplemental videos. Submitted to Physical Review Letters

Ion-ion correlations, screening, and equilibrium bulk structure in various concentrated electrolytes are investigated using synchrotron small angle X-ray scattering (SAXS), theory, and molecular simulation. Utilizing SAXS measurements we provide estimates of the Kirkwood Transition (KT) for a variety of aqueous electrolytes (NaCl, CaCl$_2$, SrCl$_2$, and ErCl$_3$). The KT may be defined as the concentration above which the ion-ion correlations cease to decay exponentially with a single length scale given by the Debye length $\lambda_{\rm D}$ and develop an additional length scale, $d=2\pi/Q_0$ that reflects the formation of local domains of charge. Theoretical models of the KT have been known for decades for highly idealized models of electrolytes, but experimental verification of KT in real electrolytes has yet to be confirmed. Herein, we provide consistent theoretical and experimental estimates of both the inverse screening lengths $a_0$ and inverse domain size, $Q_0$ for the aforementioned electrolyte systems. Taken together, $a_0$ and $Q_0$ are known descriptors of the KT and provide a view into the complexity of ion-ion interaction beyond the well-accepted Debye-H\"{u}ckel limit. Our findings suggest a picture of interaction for real electrolytes that is more general than that found in idealized models that is manifest in the precise form of the non-local response function that we estimate through the interpretation of the experimental SAXS signal. Importantly, the additional complexity of describing ion-ion interaction of real electrolytes will implicate the short-range ion-ion interactions that can only be computed via molecular simulation and provide a quantitative approach to describe electrolyte phenomena beyond Debye-H\"{u}ckel theory., Comment: 35

Numerical simulation of turbulent fluid dynamics needs to either parameterize turbulence-which introduces large uncertainties-or explicitly resolve the smallest scales-which is prohibitively expensive. Here we provide evidence through analytic bounds and numerical studies that a potential quantum exponential speedup can be achieved to simulate the Navier-Stokes equations governing turbulence using quantum computing. Specifically, we provide a formulation of the lattice Boltzmann equation for which we give evidence that low-order Carleman linearization is much more accurate than previously believed for these systems and that for computationally interesting examples. This is achieved via a combination of reformulating the nonlinearity and accurately linearizing the dynamical equations, effectively trading nonlinearity for additional degrees of freedom that add negligible expense in the quantum solver. Based on this we apply a quantum algorithm for simulating the Carleman-linearized lattice Boltzmann equation and provide evidence that its cost scales logarithmically with system size, compared to polynomial scaling in the best known classical algorithms. This work suggests that an exponential quantum advantage may exist for simulating fluid dynamics, paving the way for simulating nonlinear multiscale transport phenomena in a wide range of disciplines using quantum computing.

We study the prototypical SN2 reaction Cl$^-$ + CH$_3$Cl $\to$ CH$_3$Cl + Cl$^-$ in water using quantum mechanics / molecular mechanics (QM/MM) computer simulations with transition path sampling and inertial likelihood maximization. We have identified a new solvent coordinate to complement the original atom-exchange coordinate used in the classic analysis by Chandrasekhar, Smith, and Jorgensen [Ref1]. The new solvent coordinate quantifies instantaneous solvent induced polarization relative to the equilibrium average charge density at each point along the reaction pathway. On the basis of likelihood scores and committor distributions, the new solvent coordinate improves upon the description of solvent dynamical effects relative to previously proposed solvent coordinates. However, it does not increase the transmission coefficient or the accuracy of a transition state theory rate calculation., Comment: 11 pages, 10 figures

CP2K is an open source electronic structure and molecular dynamics software package to perform atomistic simulations of solid-state, liquid, molecular and biological systems. It is especially aimed at massively-parallel and linear-scaling electronic structure methods and state-of-the-art ab-initio molecular dynamics simulations. Excellent performance for electronic structure calculations is achieved using novel algorithms implemented for modern high-performance computing systems. This review revisits the main capabilities of CP2k to perform efficient and accurate electronic structure simulations. The emphasis is put on density functional theory and multiple post-Hartree-Fock methods using the Gaussian and plane wave approach and its augmented all-electron extension., Comment: 51 pages, 5 figures

Predicting accurate NMR chemical shieldings relies upon cancellation of different types of error in the ab initio methodology used to calculate the shielding tensor of the analyte of interest and the reference. Often the intrinsic error in computed shieldings due to basis sets, approximations in the Hamiltonian, description of the wave function, and dynamic effects, is nearly identical between the analyte and reference, yet if the electronic structure or sensitivity to local environment differs dramatically, this cannot be taken for granted. Detailed prior work has examined the octahedral trivalent cation $\text{Al}(\text{H}_{2}\text{O})_{6}^{3+}$ , accounting for ab initio intrinsic errors. However, the fact that this analyte is used as a reference for the chemically distinct tetrahedral anion $\text{Al}(\text{OH})_{4}^{-}$ inspires the study of how these errors cancel in an attempt to understand the limits of predictive capability for accurately determining $^{27}\text{Al }$ shielding in $\text{Al}(\text{OH})_{4}^{-}$. In this work, we estimate the absolute shielding of $^{27}\text{Al }$ nucleus in $\text{Al}(\text{OH})_{4}^{-}$ at the coupled cluster level (515.1 $\pm$ 5.3 ppm). Shielding sensitivity to the choice of method approximation and atomic basis sets treatment has been evaluated. Solvent and thermal effects are assessed through ensemble averaging techniques using ab-initio molecular dynamics. The contribution of each type of intrinsic error is assessed for $\text{Al}(\text{H}_{2}\text{O})_{6}^{3+}$ and $\text{Al}(\text{OH})_{4}^{-}$ ions, revealing significant differences that fundamentally hamper the ability to accurately calculate the $^{27}\text{Al }$ chemical shift of $\text{Al}(\text{OH})_{4}^{-}$ from first principles., Comment: 14 pages, 6 figures

Highly concentrated or 'dense" particle suspensions can undergo a sharp increase in viscosity, or shear thickening, under applies stress. Understanding the fundamental features leading to such rheological changes in dense suspensions is crucial to optimize flow conditions or to design flow modifiers for slurry processing. While local changes to the particle environment under an applied shear can be related to changes in viscosity, there is a broader need to connect the shear thickening transition to the fundamental organization of particle-interaction forces which lead to long-range organization. In particular, at a high volume fraction of particles, recent evidence indicates frictional forces between contacting particles is of importance. Herein, the network of frictional contact forces is analyzed within simulated two-dimensional shear thickening suspensions. Two topological metrics are studied to characterize the response of the contact force network (CFN) under varying applied shear stress. The metrics, geodesic index and the void parameter, reflect complementary aspects of the CFN: one is the connectedness of the contact network and the second is the distribution of spatial areas devoid of particle-particle contacts. Considered in relation to the variation of the viscosity, the topological metrics show that the network grows homogeneously at large scales but with many local regions devoid of contacts, indicating clearly the role of stress chain growth in causing the large change in the rheological response at the shear thickening transition.

First principles molecular dynamics simulation protocol is established using revised functional of Perdew-Burke-Ernzerhof (revPBE) in conjunction with Grimme's third generation of dispersion (D3) correction to describe properties of water at ambient conditions. This study also demonstrates the consistency of the structure of water across both isobaric (NpT) and isothermal (NVT) ensembles. Going beyond the standard structural benchmarks for liquid water, we compute properties that are connected to both local structure and mass density uctuations that are related to concepts of solvation and hydrophobicity. We directly compare our revPBE results to the Becke-Lee-Yang-Parr (BLYP) plus Grimme dispersion corrections (D2) and both the empirical fixed charged model (SPC/E) and many body interaction potential model (MB-pol) to further our understanding of how the computed properties herein depend on the form of the interaction potential.

Single ion solvation free energies are one of the most important properties of electrolyte solutions and yet there is ongoing debate about what these values are. Only the values for neutral ion pairs are known. Here, we use DFT interaction potentials with molecular dynamics simulation (DFT-MD) combined with a modified version of the quasi-chemical theory (QCT) to calculate these energies for the lithium and fluoride ions. A method to correct for the error in the DFT functional is developed and very good agreement with the experimental value for the lithium fluoride pair is obtained. Moreover, this method partitions the energies into physically intuitive terms such as surface potential, cavity and charging energies which are amenable to descriptions with reduced models. Our research suggests that lithium's solvation free energy is dominated by the free energetics of a charged hard sphere, whereas fluoride exhibits significant quantum mechanical behavior that cannot be simply described with a reduced model., Comment: 13 pages, 4 figures

Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. Here, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation (DFT-MD) and isolate the effects of charge and cavitation, comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry (CHA) for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation., Comment: 28 pages, 5 figures

Thermal fluctuations cause perturbations of fluid-fluid interfaces and highly nonlinear hydrodynamics in multiphase flows. In this work, we develop a novel multiphase smoothed dissipative particle dynamics model. This model accounts for both bulk hydrodynamics and interfacial fluctuations. Interfacial surface tension is modeled by imposing a pairwise force between SDPD particles. We show that the relationship between the model parameters and surface tension, previously derived under the assumption of zero thermal fluctuation, is accurate for fluid systems at low temperature but overestimates the surface tension for intermediate and large thermal fluctuations. To analyze the effect of thermal fluctuations on surface tension, we construct a coarse-grained Euler lattice model based on the mean field theory and derive a semi-analytical formula to directly relate the surface tension to model parameters for a wide range of temperatures and model resolutions. We demonstrate that the present method correctly models the dynamic processes, such as bubble coalescence and capillary spectra across the interface.